Enum bed_reader::Index

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pub enum Index {
    All,
    One(isize),
    Vec(Vec<isize>),
    NDArray(Array1<isize>),
    VecBool(Vec<bool>),
    NDArrayBool(Array1<bool>),
    NDSliceInfo(SliceInfo1),
    RangeAny(RangeAny),
}

Expand description

A specification of which individuals (samples) or SNPs (variants) to read.

See the Table of Index Expressions for a list of expressions for selecting individuals (sample) and SNPs (variants).

By default, all individuals or SNPs are read. The indices can be specified as:

an index (negative numbers count from the end)
a vector or ndarray of indices
a Rust range (negatives not allowed)
a vector or ndarray of booleans
an ndarray slice (negative indexing and steps allowed)

Examples

use ndarray as nd;
use bed_reader::{Bed, ReadOptions, sample_bed_file};
use bed_reader::assert_eq_nan;
use ndarray::s;

let file_name = sample_bed_file("some_missing.bed")?;
let mut bed = Bed::new(file_name)?;
println!("{:?}", bed.dim()?); // prints (100, 100)

// Read all individuals and all SNPs
let val = ReadOptions::builder().f64().read(&mut bed)?;
assert!(val.dim() == (100, 100));

// Read the individual at index position 10 and all SNPs
let val = ReadOptions::builder().iid_index(10).f64().read(&mut bed)?;
assert!(val.dim() == (1, 100));

// Read the individuals at index positions 0,5, 1st-from-the-end and
// the SNP at index position 3
let val = ReadOptions::builder()
    .iid_index(vec![0, 5, -1])
    .sid_index(3)
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (3, 1));
// Repeat, but with an ndarray
let val = ReadOptions::builder()
    .iid_index(nd::array![0, 5, -1])
    .sid_index(3)
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (3, 1));
// Repeat, but with an Rust array
let val = ReadOptions::builder()
    .iid_index([0, 5, -1])
    .sid_index(3)
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (3, 1));
// Create a boolean ndarray identifying SNPs in chromosome 5,
// then select those SNPs.
let chrom_5 = bed.chromosome()?.map(|elem| elem == "5");
let val = ReadOptions::builder()
    .sid_index(chrom_5)
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (100, 6));
// Use ndarray's slice macro, [`s!`](https://docs.rs/ndarray/latest/ndarray/macro.s.html),
// to select every 2nd individual and every 3rd SNP.
let val = ReadOptions::builder()
    .iid_index(s![..;2])
    .sid_index(s![..;3])
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (50, 34));
// Use ndarray's slice macro, [`s!`](https://docs.rs/ndarray/latest/ndarray/macro.s.html),
// to select the 10th-from-last individual to the last, in reverse order,
// and every 3rd SNP in reverse order.)
let val = ReadOptions::builder()
    .iid_index(s![-10..;-1])
    .sid_index(s![..;-3])
    .f64()
    .read(&mut bed)?;
assert!(val.dim() == (10, 34));

Variants

`All`

`One(isize)`

`Vec(Vec<isize>)`

`NDArray(Array1<isize>)`

`VecBool(Vec<bool>)`

`NDArrayBool(Array1<bool>)`

`NDSliceInfo(SliceInfo1)`

`RangeAny(RangeAny)`

Implementations

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impl Index

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pub fn to_vec(&self, count: usize) -> Result<Vec<isize>, BedErrorPlus>

Turns an Index into a vector of usize indexes. Negative means count from end.

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impl Index

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pub fn len(&self, count: usize) -> Result<usize, BedErrorPlus>

Returns the number of elements in an Index.

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pub fn is_empty(&self, count: usize) -> Result<bool, BedErrorPlus>

Returns true if the Index is empty.

Trait Implementations

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impl Clone for Index

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fn clone(&self) -> Index

Returns a copy of the value. Read more

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fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more

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impl Debug for Index

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more

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